Andrea Goldsmith

Stephen Harris Professor in the School of Engineering

Electrical Engineering

Bio

Andrea Goldsmith is the Stephen Harris professor in the School of Engineering and professor of Electrical Engineering at Stanford University. She also co-founded and served as Chief Technical Officer of Plume WiFi and of Quantenna (QTNA), and she currently serves on the corporate or technical advisory boards of Crown Castle Inc. (CCI), Interdigital Corp. (IDCC), Sequans (SQNS), Quantenna (QTNA) and Cohere. Her research interests are in the design, analysis, and fundamental performance limits of wireless systems and networks, as well as in the application of communication theory and signal processing to neuroscience. Prior to Stanford she held positions at Caltech, Maxim Technologies, Memorylink Corporation, and AT&T Bell Laboratories. Dr. Goldsmith is a member of the National Academy of Engineering and the American Academy of Arts and Sciences, a Fellow of the IEEE and of Stanford, and has received several awards for her work, including the IEEE ComSoc Edwin H. Armstrong Achievement Award as well as Technical Achievement Awards in Communications Theory and in Wireless Communications, the National Academy of Engineering Gilbreth Lecture Award, and the Silicon Valley/San Jose Business Journal’s Women of Influence Award. She is author of the book ``Wireless Communications'' and co-author of the books ``MIMO Wireless Communications'' and “Principles of Cognitive Radio,” all published by Cambridge University Press, as well as an inventor on 28 patents. She has served in various leadership roles in the IEEE and in industrial groups aimed at diversifying STEM fields. At Stanford she has served as Chair and a member of the Faculty Senate and on the Planning and Policy Board, Committee on Research, Commissions on Graduate Education and on Undergraduate Education, and the Task Force on Women and Leadership. She currently serves on Stanford's Budget Group, Advisory Board, Faculty Women's Forum Steering Committee, and in the Faculty Senate.

Abstract

Identification of genomic patterns in tumors is an important problem, which would enable the community to understand and extend effective therapies across the current tissue-based tumor boundaries. With this in mind, in this work we develop a robust and fast algorithm to discover cancer driver genes using an unsupervised clustering of similarly expressed genes across cancer patients. Specifically, we introduce CaMoDi, a new method for module discovery which demonstrates superior performance across a number of computational and statistical metrics.The proposed algorithm CaMoDi demonstrates effective statistical performance compared to the state of the art, and is algorithmically simple and scalable - which makes it suitable for tissue-independent genomic characterization of individual tumors as well as groups of tumors. We perform an extensive comparative study between CaMoDi and two previously developed methods (CONEXIC and AMARETTO), across 11 individual tumors and 8 combinations of tumors from The Cancer Genome Atlas. We demonstrate that CaMoDi is able to discover modules with better average consistency and homogeneity, with similar or better adjusted R2 performance compared to CONEXIC and AMARETTO.We present a novel method for Cancer Module Discovery, CaMoDi, and demonstrate through extensive simulations on the TCGA Pan-Cancer dataset that it achieves comparable or better performance than that of CONEXIC and AMARETTO, while achieving an order-of-magnitude improvement in computational run time compared to the other methods.

Abstract

Rectally applied antiretroviral microbicides for preexposure prophylaxis (PrEP) of HIV infection are currently in development. Since enemas (rectal douches) are commonly used by men who have sex with men prior to receptive anal intercourse, a microbicide enema could enhance PrEP adherence by fitting seamlessly within the usual sexual practices. We assessed the distribution, safety, and acceptability of three enema types-hyperosmolar (Fleet), hypoosmolar (distilled water), and isoosmolar (Normosol-R)-in a crossover design. Nine men received each enema type in random order. Enemas were radiolabeled [(99m)Tc-diethylene triamine pentaacetic acid (DTPA)] to assess enema distribution in the colon using single photon emission computed tomography/computed tomography (SPECT/CT) imaging. Plasma (99m)Tc-DTPA indicated mucosal permeability. Sigmoidoscopic colon tissue biopsies were taken to assess injury as well as tissue penetration of the (99m)Tc-DTPA. Acceptability was assessed after each product use and at the end of the study. SPECT/CT imaging showed that the isoosmolar enema had greater proximal colonic distribution (up to the splenic flexure) and greater luminal and colon tissue concentrations of (99m)Tc-DTPA when compared to the other enemas (p<0.01). Colon biopsies also showed that only the hyperosmolar enema caused sloughing of the colonic epithelium (p<0.05). In permeability testing, the hypoosmolar enema had higher plasma (99m)Tc-DTPA 24-h area under the concentration-time curve and peak concentration compared to the hyperosmolar and isoosmolar enemas, respectively. Acceptability was generally good with no clear preferences among the three enema types. The isoosmolar enema was superior or similar to the other enemas in all categories and is a good candidate for further development as a rectal microbicide vehicle.

Abstract

Gene expression analysis is generally performed on heterogeneous tissue samples consisting of multiple cell types. Current methods developed to separate heterogeneous gene expression rely on prior knowledge of the cell-type composition and/or signatures--these are not available in most public datasets. We present a novel method to identify the cell-type composition, signatures and proportions per sample without need for a-priori information. The method was successfully tested on controlled and semi-controlled datasets and performed as accurately as current methods that do require additional information. As such, this method enables the analysis of cell-type specific gene expression using existing large pools of publically available microarray datasets.

Coding Strategies for a Class of Decentralized Control Problems with Limited Communication50th IEEE Conference of Decision and Control (CDC)/European Control Conference (ECC)Mirghaderi, R., Lall, S., Goldsmith, A.IEEE.2011: 4809–4816

Abstract

To evaluate spasticity under controlled velocities and torques in children with cerebral palsy (CP) using a manual spasticity evaluator.The study involved 10 children with spastic CP (six males, four females; mean age 10 y 1 mo, SD 2 y 9 mo, range 7-16 y; one with quadriplegia, six with right hemiplegia, three with left hemiplegia; Gross Motor Function Classification System levels I [n=2], II [n=3], III [n=2], IV [n=2], and V [n=1]; Manual Ability Classification System levels II [n=5], III [n=4], and V [n=1]) and 10 typically developing participants (four males, six females; mean age 10 y 3 mo, SD 2 y 7 mo, range 7-15 y). Spasticity and catch angle were evaluated using joint position, resistance torque, and torque rate at velocities of 90 degrees, 180 degrees, and 270 degrees per second, controlled using real-time audio-visual feedback. Biomechanically, elbow range of motion (ROM), stiffness, and energy loss were determined during slow movement (30 degrees/s) and under controlled terminal torque.Compared with typically developing children, children with CP showed higher reflex-mediated torque (p<0.001) and the torque increased more rapidly with increasing velocity (p<0.001). Catch angle was dependent on velocity and occurred later with increasing velocity (p=0.005). Children with CP showed smaller ROM (p<0.05), greater stiffness (p<0.001), and more energy loss (p=0.003).Spasticity with velocity dependence may also be position-dependent. The delayed catch angle at higher velocities indicates that the greater resistance felt by the examiner at higher velocities was also due to position change, because the joint was moved further to a stiffer position at higher velocities.

Abstract

Viral infection is associated with approximately one-half of acute exacerbations of chronic obstructive pulmonary disease (COPD), which in turn, accelerate disease progression. In this study, we infected mice exposed to a combination of elastase and LPS, a constituent of cigarette smoke and a risk factor for development of COPD, with rhinovirus serotype 1B, and examined animals for viral persistence, airway resistance, lung volume, and cytokine responses. Mice exposed to elastase and LPS once a week for 4 wk showed features of COPD such as airway inflammation and obstruction, goblet cell metaplasia, reduced lung elastance, increased total lung volume, and increased alveolar chord length. In general, mice exposed to elastase or LPS alone showed intermediate effects. Compared with rhinovirus (RV)-infected PBS-exposed mice, RV-infected elastase/LPS-exposed mice showed persistence of viral RNA, airway hyperresponsiveness, increased lung volume, and sustained increases in expression of TNFalpha, IL-5, IL-13, and muc5AC (up to 14 days postinfection). Furthermore, virus-induced IFNs, interferon response factor-7, and IL-10 were deficient in elastase/LPS-treated mice. Mice exposed to LPS or elastase alone cleared virus similar to PBS-treated control mice. We conclude that limited exposure of mice to elastase/LPS produces a COPD-like condition including increased persistence of RV, likely due to skewing of the immune response towards a Th2 phenotype. Similar mechanisms may be operative in COPD.

Oblivious Equilibrium: An Approximation to Large Population Dynamic Games with Concave UtilityInternational Conference on Game Theory for NetworksAdlakha, S., Johari, R., Weintraub, G., Goldsmith, A.IEEE.2009: 68–69

On the capacity of the vector MAC with feedback41st Annual Allerton Conference on Communication, Control and ComputingJafar, S., Goldsmith, A.IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC.2006: 3259–64

wireless communication systems. From the beginning of 2006 he is serving as the vice-chair of Working Group 5 (short-range communications) for the Wireless World Research Forum (WWRF). AndersBrødløsOlsenreceivedhisM. Sc. EE degree insignalprocessingwith specialization in Applied Signal Processing and Implementation from AalborgCooperation in Wireless Networks: Principles and Applications: Real Egoistic ...Goldsmith, A. J.2006

Abstract

Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.

Abstract

Hematopoietic stem cells (HSCs) have self-renewal capacity and multilineage developmental potentials. The molecular mechanisms that control the self-renewal of HSCs are still largely unknown. Here, a systematic approach using bioinformatics and array hybridization techniques to analyze gene expression profiles in HSCs is described. To enrich mRNAs predominantly expressed in uncommitted cell lineages, 54 000 cDNA clones generated from a highly enriched population of HSCs and a mixed population of stem and early multipotent progenitor (MPP) cells were arrayed on nylon membranes (macroarray or high-density array), and subtracted with cDNA probes derived from mature lineage cells including spleen, thymus, and bone marrow. Five thousand cDNA clones with very low hybridization signals were selected for sequencing and further analysis using microarrays on glass slides. Two populations of cells, HSCs and MPP cells, were compared for differential gene expression using microarray analysis. HSCs have the ability to self-renew, while MPP cells have lost the capacity for self-renewal. A large number of genes that were differentially expressed by enriched populations of HSCs and MPP cells were identified. These included transcription factors, signaling molecules, and previously unknown genes.